title: GOTM Simulation ows_papa                  # simulation title used in output [default=GOTM simulation]
location:
   name: Ocean Weather Station Papa     # station name used in output [default=GOTM site]
   latitude: 50.0                       # latitude [degrees North; min=-90.0; max=90.0; default=0.0]
   longitude: -145.0                    # longitude [degrees East; min=-360.0; max=360.0; default=0.0]
   depth: 250.0                         # water depth [m; min=0.0; default=100.0]
time:
   start: 1961-03-25 00:00:00           # start date and time [yyyy-mm-dd HH:MM:SS; default=2017-01-01 00:00:00]
   stop: 1962-03-25 00:00:00            # stop date and time [yyyy-mm-dd HH:MM:SS; default=2018-01-01 00:00:00]
   dt: 3600.0                           # time step for integration [s; min=0.0; default=3600.0]
grid:
   nlev: 250                            # number of layers [min=1; default=100]
   method: 0                            # layer thicknesses [0=equal by default with optional zooming, 1=prescribed relative fractions, 2=prescribed thicknesses; default=0]
   ddu: 0.0                             # surface zooming [dimensionless; min=0.0; default=0.0]
   ddl: 0.0                             # bottom zooming [dimensionless; min=0.0; default=0.0]
   file:                                # file with custom grid [default=]
temperature:                            # temperature profile used for initialization and optionally relaxation
   method: 2                            # method [0=off, 1=analytical, 2=from file; default=0]
   file: t_prof_file.dat                # path to file with series of profiles [default=]
   column: 1                            # index of column to read from [default=1]
   analytical:
      method: 3                         # type of analytical initial temperature profile [1=constant, 2=two layers, 3=from salinity and buoyancy frequency; default=1]
      z_t1: 30.0                        # upper layer thickness [m; min=0.0; default=0.0]
      t_1: 20.0                         # upper layer temperature [Celsius; min=0.0; max=40.0; default=0.0]
      z_t2: 40.0                        # lower layer thickness [m; min=0.0; default=0.0]
      t_2: 15.0                         # lower layer temperature [Celsius; min=0.0; max=40.0; default=0.0]
      obs_NN: 2.56000000E-04            # constant buoyancy frequency [s^-2; min=0.0; default=0.0]
   relax:                               # relax model temperature to observed/prescribed value
      tau: 1.00000000E+15               # time scale for interior layer [s; min=0.0; default=1.00000000E+15]
salinity:                               # salinity profile used for initialization and optionally relaxation
   method: 2                            # method [0=off, 1=analytical, 2=from file; default=0]
   file: s_prof_file.dat                # path to file with series of profiles [default=]
   column: 1                            # index of column to read from [default=1]
   analytical:
      method: 1                         # type of analytical initial salinity profile [1=constant, 2=two layers, 3=from temperature and buoyancy frequency; default=1]
      z_s1: 30.0                        # upper layer thickness [m; min=0.0; default=0.0]
      s_1: 20.0                         # upper layer salinity [psu; min=0.0; max=40.0; default=0.0]
      z_s2: 40.0                        # lower layer thickness [m; min=0.0; default=0.0]
      s_2: 15.0                         # lower layer salinity [psu; min=0.0; max=40.0; default=0.0]
      obs_NN: 2.56000000E-04            # constant buoyancy frequency [s^-2; min=0.0; default=0.0]
   relax:                               # relax model salinity to observed/prescribed value
      tau: 86400.0                      # time scale for interior layer [s; min=0.0; default=1.00000000E+15]
      tau_s: 86400.0                    # time scale for surface layer [s; min=0.0; default=1.00000000E+15]
      tau_b: 86400.0                    # time scale for bottom layer [s; min=0.0; default=1.00000000E+15]
surface:
   fluxes:                              # heat and momentum fluxes
      method: 0                         # method to calculate fluxes from meteorology [0=use prescribed fluxes, 1=Kondo (1975), 2=Fairall et al. (1996); default=0]
      heat:                             # prescribed total heat flux (sensible, latent and net back-radiation)
         method: 2                      # method [0=constant, 2=from file; default=0]
         constant_value: 0.0            # value to use throughout the simulation [W/m^2; default=0.0]
         file: heatflux_file.dat        # path to file with time series [default=]
         column: 1                      # index of column to read from [default=1]
      tx:                               # prescribed momentum flux in West-East direction
         method: 2                      # method [0=constant, 2=from file; default=0]
         constant_value: 0.0            # value to use throughout the simulation [Pa; default=0.0]
         file: momentumflux_file.dat    # path to file with time series [default=]
         column: 1                      # index of column to read from [default=1]
      ty:                               # prescribed momentum flux in South-North direction
         method: 2                      # method [0=constant, 2=from file; default=0]
         constant_value: 0.0            # value to use throughout the simulation [Pa; default=0.0]
         file: momentumflux_file.dat    # path to file with time series [default=]
         column: 2                      # index of column to read from [default=1]
   meteo:
      u10:                              # wind speed in West-East direction @ 10 m
         method: 2                      # method [0=constant, 2=from file; default=0]
         constant_value: 0.0            # value to use throughout the simulation [m/s; default=0.0]
         file:                          # path to file with time series [default=]
         column: 1                      # index of column to read from [default=1]
      v10:                              # wind speed in South-North direction @ 10 m
         method: 2                      # method [0=constant, 2=from file; default=0]
         constant_value: 0.0            # value to use throughout the simulation [m/s; default=0.0]
         file:                          # path to file with time series [default=]
         column: 2                      # index of column to read from [default=1]
      airp:                             # air pressure
         method: 2                      # method [0=constant, 2=from file; default=0]
         constant_value: 0.0            # value to use throughout the simulation [Pa; default=0.0]
         file:                          # path to file with time series [default=]
         column: 3                      # index of column to read from [default=1]
         scale_factor: 100.0            # scale factor to be applied to values read from file [default=1.0]
      airt:                             # air temperature @ 2 m
         method: 2                      # method [0=constant, 2=from file; default=0]
         constant_value: 0.0            # value to use throughout the simulation [Celsius or K; default=0.0]
         file:                          # path to file with time series [default=]
         column: 4                      # index of column to read from [default=1]
      hum:                              # humidity @ 2 m
         method: 2                      # method [0=constant, 2=from file; default=0]
         constant_value: 0.0            # value to use throughout the simulation [default=0.0]
         file:                          # path to file with time series [default=]
         column: 5                      # index of column to read from [default=1]
         type: 1                        # humidity metric [1=relative humidity (%), 2=wet-bulb temperature, 3=dew point temperature, 4=specific humidity (kg/kg); default=1]
      cloud:                            # cloud cover
         method: 2                      # method [0=constant, 2=from file; default=0]
         constant_value: 0.0            # value to use throughout the simulation [fraction; min=0.0; max=1.0; default=0.0]
         file:                          # path to file with time series [default=]
         column: 6                      # index of column to read from [default=1]
      swr:                              # shortwave radiation
         method: 2                      # method [0=constant, 2=from file, 3=from time, location and cloud cover; default=0]
         constant_value: 0.0            # value to use throughout the simulation [W/m^2; min=0.0; default=0.0]
         file: swr_file.dat             # path to file with time series [default=]
         column: 1                      # index of column to read from [default=1]
      precip:                           # precipitation
         method: 0                      # method [0=constant, 2=from file; default=0]
         constant_value: 0.0            # value to use throughout the simulation [m/s; default=0.0]
         file:                          # path to file with time series [default=]
         column: 1                      # index of column to read from [default=1]
         flux_impact: false             # include effect on fluxes of sensible heat and momentum [default=false]
      calc_evaporation: false           # calculate evaporation from meteorological conditions [default=false]
      ssuv_method: 0                    # wind treatment [0=use absolute wind speed, 1=use wind speed relative to current velocity; default=1]
   longwave_radiation:                  # net longwave radiation
      method: 1                         # method [0=from file, 1=Clark, 2=Hastenrath, 3=Bignami, 4=Berliand, 5=Josey-1, 6=Josey-2; default=1]
      file:                             # path to file with time series [default=]
      column: 1                         # index of column to read from [default=1]
   albedo:
      method: 0                         # method to compute albedo [0=constant, 1=Payne (1972), 2=Cogley (1979); default=1]
      constant_value: 0.0               # constant value to use throughout the simulation [fraction; min=0.0; max=1.0; default=0.0]
   sst:                                 # observed surface temperature
      method: 2                         # method [0=constant, 2=from file; default=0]
      file: sst_file.dat                # path to file with time series [default=]
   roughness:
      charnock: false                   # use Charnock (1955) roughness adaptation [default=false]
      charnock_val: 1400.0              # empirical constant for roughness adaptation [dimensionless; min=0.0; default=1400.0]
      z0s_min: 0.02                     # hydrodynamic roughness (minimum value if Charnock adaptation is used) [m; min=0.0; default=0.02]
bottom:
   h0b: 0.05                            # physical bottom roughness [m; min=0.0; default=0.05]
light_extinction:
   method: 1                            # water type [1=Jerlov type I, 2=Jerlov type 1 (upper 50 m), 3=Jerlov type IA, 4=Jerlov type IB, 5=Jerlov type II, 6=Jerlov type III, 7=custom; default=1]
   A:                                   # non-visible fraction of shortwave radiation
      method: 0                         # method [0=constant, 2=from file; default=0]
      constant_value: 0.7               # value to use throughout the simulation [fraction; min=0.0; max=1.0; default=0.7]
      file:                             # path to file with time series [default=]
      column: 1                         # index of column to read from [default=1]
   g1:                                  # e-folding depth of non-visible shortwave radiation
      method: 0                         # method [0=constant, 2=from file; default=0]
      constant_value: 0.4               # value to use throughout the simulation [m; min=0.0; default=0.4]
      file:                             # path to file with time series [default=]
      column: 1                         # index of column to read from [default=1]
   g2:                                  # e-folding depth of visible shortwave radiation
      method: 0                         # method [0=constant, 2=from file; default=0]
      constant_value: 8.0               # value to use throughout the simulation [m; min=0.0; default=8.0]
      file:                             # path to file with time series [default=]
      column: 1                         # index of column to read from [default=1]
turbulence:
   turb_method: 3                       # turbulence closure [0=convective adjustment, 2=first-order, 3=second-order; default=3]
   tke_method: 2                        # turbulent kinetic energy equation [1=algebraic length scale equation, 2=differential equation for tke (k-epsilon style), 3=differential equation for q^2/2 (Mellor-Yamada style); default=2]
   len_scale_method: 8                  # dissipative length scale [1=parabolic, 2=triangular, 3=Xing and Davies (1995), 4=Robert and Ouellet (1987), 5=Blackadar (two boundaries) (1962), 6=Bougeault and Andre (1986), 7=Eifler and Schrimpf (ISPRAMIX) (1992), 8=dynamic dissipation rate equation, 9=dynamic Mellor-Yamada q^2 l-equation, 10=generic length scale (GLS); default=8]
   stab_method: 3                       # stability functions [1=constant, 2=Munk and Anderson (1954), 3=Schumann and Gerz (1995), 4=Eifler and Schrimpf (1992); default=1]
   turb_param:
      cm0_fix: 5.47700000E-01           # value of cm0 [dimensionless; min=0.0; default=5.47700000E-01]
      Prandtl0_fix: 0.74                # turbulent Prandtl-number [dimensionless; min=0.0; default=0.74]
      cw: 100.0                         # constant of the wave-breaking model [dimensionless; min=0.0; default=100.0]
      compute_kappa: false              # compute von Karman constant from model parameters [default=false]
      kappa: 0.4                        # von Karman constant [dimensionless; min=0.0; default=0.4]
      compute_c3: true                  # compute c3 (E3 for Mellor-Yamada) from steady-state Richardson number [default=true]
      Ri_st: 0.25                       # desired steady-state Richardson number [dimensionless; min=0.0; default=0.25]
      length_lim: true                  # apply Galperin et al. (1988) length scale limitation [default=true]
      galp: 0.53                        # coefficient for length scale limitation [dimensionless; min=0.0; default=0.27]
      const_num: 1.00000000E-04         # constant eddy diffusivity [m^2/s; min=0.0; default=5.00000000E-04]
      const_nuh: 1.00000000E-04         # constant heat diffusivity [m^2/s; min=0.0; default=5.00000000E-04]
      k_min: 1.00000000E-06             # minimum turbulent kinetic energy [m^2/s^2; min=0.0; default=1.00000000E-10]
      eps_min: 1.00000000E-12           # minimum dissipation rate [m^2/s^3; min=0.0; default=1.00000000E-12]
      kb_min: 1.00000000E-10            # minimum buoyancy variance [m^2/s^4; min=0.0; default=1.00000000E-10]
      epsb_min: 1.00000000E-14          # minimum buoyancy variance destruction rate [m^2/s^5; min=0.0; default=1.00000000E-14]
   generic:                             # generic length scale (GLS) model
      gen_m: 1.0                        # exponent for k [dimensionless; default=1.5]
      gen_n: -0.67                      # exponent for l [dimensionless; default=-1.0]
      cpsi1: 1.0                        # empirical coefficient cpsi1 in psi equation [dimensionless; default=1.44]
      cpsi2: 1.22                       # empirical coefficient cpsi2 in psi equation [dimensionless; default=1.92]
      cpsi3minus: 0.05                  # cpsi3 for stable stratification [dimensionless; default=0.0]
      sig_kpsi: 0.8                     # Schmidt number for TKE diffusivity [dimensionless; default=1.0]
      sig_psi: 1.07                     # Schmidt number for psi diffusivity [dimensionless; default=1.3]
   keps:                                # k-epsilon model
      ce3minus: -0.4                    # ce3 for stable stratification [dimensionless; default=0.0]
   my:                                  # Mellor-Yamada model
      length: 3                         # barotropic length scale in q^2 l equation [1=parabolic, 2=triangular, 3=linear from surface; default=1]
   scnd:                                # second-order model
      method: 1                         # method [1=quasi-equilibrium, 2=weak equilibrium with algebraic buoyancy variance; default=2]
      scnd_coeff: 7                     # coefficients of second-order model [0=custom, 1=Gibson and Launder (1978), 2=Mellor and Yamada (1982), 3=Kantha and Clayson (1994), 4=Luyten et al. (1996), 5=Canuto et al. (2001) (version A), 6=Canuto et al. (2001) (version B), 7=Cheng et al. (2002); default=5]
   iw:                                  # internal wave mixing
      model: 2                          # model [0=none, 1=Mellor (1989), 2=Large et al. (1994); default=0]
      alpha: 0.7                        # coefficient for Mellor internal wave model [dimensionless; default=0.0]
mimic_3d:                               # effects of horizontal gradients
   ext_pressure:                        # external pressure
      mode: 0                           # formulation [0=horizontal gradient in surface elevation, 1=horizontal velocities at given height above bed, 2=vertically averaged horizontal velocities; default=0]
      dpdx:                             # pressure in West-East direction
         method: 0                      # method [0=constant, 1=from tidal constituents, 2=from file; default=0]
         constant_value: 0.0            # value to use throughout the simulation [default=0.0]
         file:                          # path to file with time series [default=]
         column: 1                      # index of column to read from [default=1]
         AmpM: 0.0                      # amplitude of 1st harmonic [dimensionless; default=0.0]
         PhaseM: 0.0                    # phase of 1st harmonic [s; min=0.0; default=0.0]
         AmpS: 0.0                      # amplitude of 2nd harmonic [dimensionless; default=0.0]
         PhaseS: 0.0                    # phase of 2nd harmonic [s; min=0.0; default=0.0]
      dpdy:                             # pressure in South-North direction
         method: 0                      # method [0=constant, 1=from tidal constituents, 2=from file; default=0]
         constant_value: 0.0            # value to use throughout the simulation [default=0.0]
         file:                          # path to file with time series [default=]
         column: 1                      # index of column to read from [default=1]
         AmpM: 0.0                      # amplitude of 1st harmonic [dimensionless; default=0.0]
         PhaseM: 0.0                    # phase of 1st harmonic [s; min=0.0; default=0.0]
         AmpS: 0.0                      # amplitude of 2nd harmonic [dimensionless; default=0.0]
         PhaseS: 0.0                    # phase of 2nd harmonic [s; min=0.0; default=0.0]
      h:                                # height above bed
         method: 0                      # method [0=constant, 2=from file; default=0]
         constant_value: 0.0            # value to use throughout the simulation [m; min=0.0; default=0.0]
         file:                          # path to file with time series [default=]
         column: 1                      # index of column to read from [default=1]
      PeriodM: 44714.0                  # period of 1st tidal harmonic (eg. M2-tide) [s; default=44714.0]
      PeriodS: 43200.0                  # period of 2nd tidal harmonic (eg. S2-tide) [s; default=43200.0]
   int_press:                           # internal pressure
      dtdx:                             # temperature gradient in West-East direction
         method: 0                      # method [0=off, 1=constant, 2=from file; default=0]
         constant_value: 0.0            # value to use throughout the simulation [Celsius/m; default=0.0]
         file:                          # path to file with series of profiles [default=]
         column: 1                      # index of column to read from [default=1]
      dtdy:                             # temperature gradient in South-North direction
         method: 0                      # method [0=off, 1=constant, 2=from file; default=0]
         constant_value: 0.0            # value to use throughout the simulation [Celsius/m; default=0.0]
         file:                          # path to file with series of profiles [default=]
         column: 1                      # index of column to read from [default=1]
      dsdx:                             # salinity gradient in West-East direction
         method: 0                      # method [0=off, 1=constant, 2=from file; default=0]
         constant_value: 0.0            # value to use throughout the simulation [psu/m; default=0.0]
         file:                          # path to file with series of profiles [default=]
         column: 1                      # index of column to read from [default=1]
      dsdy:                             # salinity gradient in South-North direction
         method: 0                      # method [0=off, 1=constant, 2=from file; default=0]
         constant_value: 0.0            # value to use throughout the simulation [psu/m; default=0.0]
         file:                          # path to file with series of profiles [default=]
         column: 1                      # index of column to read from [default=1]
      t_adv: false                      # horizontally advect temperature [default=false]
      s_adv: false                      # horizontally advect salinity [default=false]
   zeta:                                # surface elevation
      method: 0                         # method [0=constant, 1=from tidal constituents, 2=from file; default=0]
      constant_value: 0.0               # value to use throughout the simulation [m; default=0.0]
      file:                             # path to file with time series [default=]
      column: 1                         # index of column to read from [default=1]
      period_1: 44714.0                 # period of 1st harmonic (eg. M2-tide) [s; default=44714.0]
      amp_1: 1.0                        # amplitude of 1st harmonic [m; default=0.0]
      phase_1: 0.0                      # phase of 1st harmonic [s; min=0.0; default=0.0]
      period_2: 43200.0                 # period of 2nd harmonic (eg. S2-tide) [s; default=43200.0]
      amp_2: 0.5                        # amplitude of 2nd harmonic [m; default=0.0]
      phase_2: 0.0                      # phase of 2nd harmonic [s; min=0.0; default=0.0]
   w:                                   # vertical velocity
      max:                              # maximum velocity
         method: 0                      # method [0=off, 1=constant, 2=from file; default=0]
         constant_value: 0.0            # value to use throughout the simulation [m/s; default=0.0]
         file:                          # path to file with time series [default=]
         column: 1                      # index of column to read from [default=1]
      height:                           # height of maximum velocity
         method: 1                      # method [1=constant, 2=from file; default=1]
         constant_value: 0.0            # value to use throughout the simulation [m; default=0.0]
         file:                          # path to file with time series [default=]
         column: 1                      # index of column to read from [default=1]
      adv_discr: 6                      # vertical advection scheme [1=first-order upstream, 3=third-order upstream-biased polynomial, 4=third-order TVD with Superbee limiter, 5=third-order TVD with MUSCL limiter, 6=third-order TVD with ULTIMATE QUICKEST limiter; default=6]
velocities:                             # observed/prescribed horizontal velocities
   u:                                   # velocity in West-East direction
      method: 0                         # method [0=off, 2=from file; default=0]
      file:                             # path to file with series of profiles [default=]
      column: 1                         # index of column to read from [default=1]
   v:                                   # velocity in South-North direction
      method: 0                         # method [0=off, 2=from file; default=0]
      file:                             # path to file with series of profiles [default=]
      column: 1                         # index of column to read from [default=1]
   relax:                               # relax model velocities towards observed/prescribed value
      tau: 1.00000000E+15               # time scale [s; min=0.0; default=1.00000000E+15]
      ramp: 1.00000000E+15              # duration of initial relaxation period [s; min=0.0; default=1.00000000E+15]
o2:                                     # oxygen
   scale_factor: 31.25                  # scale factor to be applied to values read from file [default=1.0]
buoyancy:
   NN_ini: 1.00000000E-04               # initial value of NN (=buoyancy gradient) [s^-2; default=0.0]
eq_state:                               # equation of state
   mode: 1                              # formula [1=UNESCO, 2=Jackett et al. (2005); default=2]
   method: 1                            # implementation [1=full with in-situ temperature/density, 2=full with potential temperature/density, 3=linearized at T0,S0,p0, 4=linearized at T0,S0,p0,dtr0,dsr0; default=1]
   T0: 10.0                             # reference temperature [Celsius; min=-2.0; default=10.0]
   S0: 35.0                             # reference salinity [psu; min=0.0; default=35.0]
   p0: 0.0                              # reference pressure [Pa; default=0.0]
   dtr0: -0.17                          # thermal expansion coefficient [kg/m^3/K; default=-0.17]
   dsr0: 0.78                           # saline expansion coefficient [kg/m^3/psu; default=0.78]
restart:
   load: false                          # initialize simulation with state stored in restart.nc [default=false]
output:
   ows_papa:                            # path of output file, excluding extension
      format: netcdf                    # format [text, netcdf; default=netcdf]
      time_unit: dt                     # time unit [second, hour, day, month, year, dt=model time step; default=day]
      time_step: 24                     # number of time units between output [min=1; default=1]
      time_method: point                # treatment of time dimension [point=instantaneous, mean, integrated; default=point]
      variables:
      - source: *                       # variable name in model
